Applying rotation mess up model
The correct way to apply a pose of a rigged character is: pose the model in its desired rest pose; select the mesh and apply its armature modifier; select the armature and in pose mode select all bones and press Ctrl A &quot;Apply pose as rest pose&quot;; add to the mesh a new armature modifier, pointing a the armature rig.
This procedure will not affect the weights, but can destroy any previously made animation.